NEW TOOLS FOR EXPLORING THE DYNAMIC INTERACTOME

探索动态交互组的新工具

• 批准号: 8173583
• 负责人: MICHAEL P ROUT
• 金额: $ 330.42万
• 依托单位: ROCKEFELLER UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-08-15 至 2011-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8173583
• 关键词: Area; Biological; Cell Nucleus; Cell physiology; Cells; Cellular biology; Chromatin; Communities; Complex; Computational Biology; Computer Retrieval of Information on Scientific Projects Database; Coupling; Cytomegalovirus; Dancing; Data; Eukaryota; Freezing; Funding; Genetic; Genetic Transcription; Genome; Genomics; Grant; HIV; Hand; Human Virus; Institution; Laboratories; Macromolecular Complexes; Mass Spectrum Analysis; Methods; Nucleic Acids; Pathway interactions; Positioning Attribute; Process; Production; Property; Proteins; Proteomics; RNA; Research; Research Personnel; Resources; Source; Staging; Stretching; Structural Protein; Structure; System; Systems Biology; Techniques; Technology; Testing; Time; United States National Institutes of Health; Walking; empowered; functional genomics; macromolecule; novel strategies; rapid technique; software development; tool

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. DESCRIPTION (provided by applicant): The genomic revolution has been empowered by technologies that have determined a vast pool of genetic information. While nucleic acids encode this information, it is the proteins that act on it. Proteins are incredibly diverse in their abundance & their properties, making them highly versatile for the dynamic tasks at hand but at the same time exceptionally difficult to analyze. It is for these reasons that the proteomic revolution still lags behind the genomic revolution. Indeed, the comprehensive analysis of the dynamic properties of proteins in cells is still largely beyond current capabilities. Here, we seek to revolutionize proteomics by synergistically combining improvements in established techniques with new approaches. We will overcome major bottlenecks in 3 key areas of proteomics technology. First, we will reform the production stage for generating intact macromolecular complexes, so that we will be able to freeze a tagged macromolecular complex in place, within moments of visualizing its position in the cell, & then isolate it together with all its components & neighbors. Second, we will optimize the analysis of each complex such that its macromolecular composition, structure, & dynamics will be quantified & analyzed. Third, we will develop software to integrate our data & represent in unprecedented detail the actions of the macromolecular players in many dynamic subcellular assemblies. We will seek to make these techniques rapid, robust & routine by beta testing them in 4 experimental systems. These systems focus on aspects of the genetic information pathway, because (i) this is core to eukaryotes, & (ii) it will allow us to develop techniques to analyze the interactions of all 3 information-carrying biological macromolecules (DMA, RNA & proteins). First, we will walk along great stretches of chromatin, determining the normal flux of structural proteins & regulatory factors that together comprise dynamic segments of the genome. Second, we will follow the course of RNA after transcription, as it is processed, packaged & exported from the nucleus; we will enumerate the proteins that dance attendance on each kind of RNA molecule during its maturation. Finally, we will expose how 2 pathogenic human viruses, HIV & CMV, subvert their host's genetic information pathway & supplant it with their own. By creating a National Center for Dynamic Interactome Research, we will be coupling an established mass spectrometry resource, cell biology laboratories, a systems biology resource, & a computational biology center. As part of the larger NIH roadmap, the center's aim will be to create new & useful tools to elucidate the dynamics of macromolecular interactions. In summary, the present proposal seeks the support to advance our methods into totally new areas, & to spread these methods amongst the biomedical community. The Center will enable the community to assemble the kinds of detailed, dynamic representations of the interactions in the cell that will help elucidate the principles underlying all cellular processes, thus bridging the gaps between functional genomics, proteomics, & systems biology.

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目及 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 描述（由申请人提供）：基因组革命得到了确定大量遗传信息的技术的支持。虽然核酸编码这些信息，但作用于它的是蛋白质。蛋白质的丰度和特性极其多样化，这使得它们对于当前的动态任务具有高度的通用性，但同时又异常难以分析。正是由于这些原因，蛋白质组革命仍然落后于基因组革命。事实上，对细胞中蛋白质动态特性的综合分析仍然很大程度上超出了目前的能力。在这里，我们寻求通过将现有技术的改进与新方法协同结合来彻底改变蛋白质组学。我们将攻克蛋白质组学技术3个关键领域的重大瓶颈。首先，我们将改革生成完整大分子复合物的生产阶段，以便我们能够在可视化其在细胞中的位置的瞬间将标记的大分子复合物冻结到位，然后将其与其所有组件和邻居一起分离。其次，我们将优化每个复合物的分析，以便对其大分子组成、结构和动力学进行量化和分析。第三，我们将开发软件来整合我们的数据并以前所未有的细节表示许多动态亚细胞组装中大分子参与者的行为。我们将通过在 4 个实验系统中进行 beta 测试，力求使这些技术变得快速、稳健和常规。这些系统专注于遗传信息途径的各个方面，因为（i）这是真核生物的核心，（ii）它将允许我们开发技术来分析所有 3 种携带信息的生物大分子（DMA、RNA 和蛋白质）的相互作用。首先，我们将沿着染色质的大范围行走，确定结构蛋白和调节因子的正常通量，它们共同构成基因组的动态片段。其次，我们将跟踪RNA转录后的过程，即它被加工、包装并从细胞核中输出；我们将列举在每种 RNA 分子成熟过程中参与其中的蛋白质。最后，我们将揭示两种人类致病病毒（HIV 和 CMV）如何颠覆宿主的遗传信息通路并用自己的遗传信息通路取代它。通过创建国家动态相互作用组研究中心，我们将结合现有的质谱资源、细胞生物学实验室、系统生物学资源和计算生物学中心。作为 NIH 更大路线图的一部分，该中心的目标是创造新的有用的工具来阐明大分子相互作用的动态。总之，本提案寻求支持，将我们的方法推进到全新的领域，并在生物医学界传播这些方法。该中心将使社区能够组装细胞中相互作用的各种详细的、动态的表示，这将有助于阐明所有细胞过程的原理，从而弥合功能基因组学、蛋白质组学和系统生物学之间的差距。